PDE2A p.Ile112=
c.336C>T · rs145524236 · VCV1166795
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.92%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.2 | GERP 0.46, phastCons 1 |
| Overall | ||
| CADD | 11.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.92%
South Asian · 3,567/90,902 alleles
Filtering AF
3.82%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.77%
Overall
0.58%
9,346/1,611,528 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 3.92% | 25 |
| Ashkenazi Jewishnot grpmax-eligible | 3.64% | 27 |
| Middle Eastern | 1.92% | 52 |
| Remaining individualsnot grpmax-eligible | 0.772% | 130 |
| European (non-Finnish) | 0.328% | 305 |
| Admixed American | 0.275% | 364 |
| Finnishnot grpmax-eligible | 0.06% | 1,666 |
| African / African-American | 0.0413% | 2,420 |
| East Asian | 0.00892% | 11,215 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- PDE2A
- Protein
- p.Ile112=
- Coding
- c.336C>T
- MANE Select
- NM_002599
- dbSNP
- rs145524236
- Type
- single nucleotide variant
- Location
- chr11:72597607 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 84.17 · 44 PDB
- Residue 112
- the gaf 1 domain
Similar variants
- PDE2A c.1922+4C>T Uncertain significance ★★ same type
- PDE2A p.Ala157Val Uncertain significance ★★ ⚠ same type
- PDE2A p.Ala205Val Uncertain significance ★★ ⚠ same type
- PDE2A p.Ala349Thr Uncertain significance ★★ ⚠ same type
- PDE2A p.Arg226Cys Uncertain significance ★★ ⚠ same type
- PDE2A p.Arg790Gln Uncertain significance ★★ ⚠ same type
- PDE2A p.Asp34Glu Uncertain significance ★★ ⚠ same type
- PDE2A p.Asp59Asn Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/pde2a-p-ile112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown